Improved diagnosis of Neisseria gonorrhoeae (GC) infections represents a critical unmet medical need. The CDC estimates that approximately 700,000 people are infected by GC annually, with approximately half of these cases reported. The clinical spectrum of GC infection includes urethritis and cervicitis, pelvic inflammatory disease (PID), and disseminated disease. Infection can also lead to sterility, ectopic pregnancy, and low birth weight. Approximately 10% of infected males and 50% of infected females are asymptomatic, hastening the spread of the disease. Drug resistant GC strains are a major, longstanding problem; particularly worrisome are recent reports of strains expressing decreased susceptibility or resistance to ceftriaxone. A critical obstacle to reducing the incidence of GC is the lack of an inexpensive, nucleic acid (NA)-based point-of-care (POC) diagnostic for screening. Though there are four commercially available GC assays in the US, they suffer from several limitations. Critically, they cannot be performed at the POC. Commercial tests are slow, and require extensive investment in equipment and technical expertise. Furthermore, current tests are vulnerable to mutations in the target genome that would effectively render the pathogens invisible (as was recently seen a major European Chlamydia trachomatis strain), incapable of strain typing (making reliable epidemiology studies and contact tracing impossible), and incapable of determining drug resistance profiles. NetBio is proposing to develop an inexpensive microfluidics-based diagnostic for GC that will provide sensitive and specific detection of GC to be made at the POC in real-time. Development of such an effective POC diagnostic would allow timely, appropriate treatment that would reduce the acute and chronic morbidity that is directly associated with these infections. The Specific Aims of this Phase I application are to: 1) Perform whole genome sequencing on 40 GC strains, more than tripling the available public knowledge about GC genomic structure; 2) Design a multiplexed amplification assay based on this genetic information that allows a total of 12 GC loci (including MLST and antibiotic resistance loci) to be amplified simultaneously; and 3) Perform a head-to-head test of our diagnostic against two of the leading commercial GC diagnostics. In the SBIR Phase II, we will incorporate the multiplexed amplification assay into a fully integrated system that performs DNA purification, amplification, and electrophoretic separation within 45 minutes. The first commercial product based on this work will diagnose GC based on the amplification of 12 loci, and a follow-on product will also sequence these loci. Given the genomic and sequencing expertise of Dr. Tim Read, the STD and strain-typing expertise of Drs. Dean and Shafer, and the microfluidic and molecular biology expertise of Dr. Selden, the application provides a unique collaborative opportunity to finally obtain a rapid point-of-care diagnostic for GC.